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Why are there four letters in the genetic alphabet?

Abstract

We list, without thinking, the four base types that make up DNA as adenine, guanine, cytosine and thymine. But why are there four? This question is now all the more relevant as organic chemists have synthesized new base pairs that can be incorporated into nucleic acids. Here, I argue that there are theoretical, experimental and computational reasons to believe that having four base types is a frozen relic from the RNA world, when RNA was genetic as well as enzymatic material.

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Figure 1: Base-pairing pattern of a DNA molecule.
Figure 2: Base-pairing pattern dependent on shape complementarity.
Figure 3: In silico evolution of RNA.

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Acknowledgements

I thank the biologists at the Wissenschaftskolleg zu Berlin for vivid discussions.Also, B.Papp and V.Müller who kindly read the manuscript before submission.

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FURTHER INFORMATION

Eörs Szathmáry's web page

Scripps Research Institute

Steven Benner's web page

Glossary

AMINO-A

An adenine molecule with a second amino (-NH2) group attached to its carbon in position 2, which acts as an extra hydrogen-bond donor.

DEAMINATION

The reaction of a water molecule with the amino-group on position 4 of the pyrimidine ring of cytosine, which results in the conversion of cytosine to uracil.

DIRECTIONAL SELECTION

Natural selection that acts to promote the fixation (an increase in frequency in the population to 100%) of a particular allele.

EPIMERIZATION

The spontaneous change of configuration of chemical groups that are attached to a so-called asymmetric carbon atom. Such isomers are not mirror images of each other.

ERROR-CODING THEORY

A theory that was developed by Hamming to analyse the detection and correction of errors in messages consisting of 'zeros' and 'ones'.

KLENOW FRAGMENT

The Escherichia coli DNA polymerase, without the exonuclease subunit.

MALTHUSIAN GROWTH RATE

The per capita rate of growth of a population modelled in continuous time.

MUTATION–SELECTION EQUILIBRIUM

The equilibrium at which selection that decreases the frequency of an unfavourable allele exactly balances mutations that increase its frequency.

ORTHOGONALITY

Features of natural and/or artificial bases that in a given set (alphabet) decrease the degree of incorporating non-cognate base pairs.

PROCESSIVITY

The ability of polymerases to repeatedly add bases to the primer, extending even a new type of base.

RIBO-ORGANISM

A cell in the RNA world.

RNA WORLD

A hypothetical, but widely believed, era in early evolution when RNA-like molecules were not only genetic but also enzymatic material.

SIMULATED PROTOCELL MODEL

An in silico implementation of a ribo-organism.

STABILIZING SELECTION

Selection for the mean or intermediate phenotype; consequently, peripheral variants are eliminated, which maintains an existing state of adaptation in a stable environment.

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Szathmáry, E. Why are there four letters in the genetic alphabet?. Nat Rev Genet 4, 995–1001 (2003). https://doi.org/10.1038/nrg1231

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